Skip to content

GitLab

"platforms/hip/src/HipParallelKernels.cpp" did not exist on "fe21d5ee4f14673a4ea38b7244991772a64ceec2"
Commit d4af8747 authored by peastman's avatar peastman
Browse files

Automatically select whether to use the SSE or AVX version of CpuNonbondedForce

parent 5cd23acb
Hide whitespace changes
Inline Side-by-side
Showing with 486 additions and 867 deletions
platforms/cpu/include/CpuKernels.h
View file @ d4af8747
......@@ -88,9 +88,7 @@ private:
*/
class CpuCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
CpuCalcNonbondedForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) : CalcNonbondedForceKernel(name, platform),
data(data), bonded14IndexArray(NULL), bonded14ParamArray(NULL), hasInitializedPme(false) {
}
CpuCalcNonbondedForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data);
~CpuCalcNonbondedForceKernel();
/**
* Initialize the kernel.
......@@ -130,8 +128,8 @@ private:
std::vector<std::pair<float, float> > particleParams;
std::vector<RealVec> lastPositions;
NonbondedMethod nonbondedMethod;
CpuNeighborList neighborList;
CpuNonbondedForce nonbonded;
CpuNeighborList* neighborList;
CpuNonbondedForce* nonbonded;
Kernel optimizedPme;
};
......
platforms/cpu/include/CpuNonbondedForce.h
View file @ d4af8747
......@@ -48,7 +48,13 @@ class CpuNonbondedForce {
--------------------------------------------------------------------------------------- */
CpuNonbondedForce();
/**
* Virtual destructor.
*/
virtual ~CpuNonbondedForce();
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
......@@ -151,7 +157,7 @@ class CpuNonbondedForce {
*/
void threadComputeDirect(ThreadPool& threads, int threadIndex);
private:
protected:
bool cutoff;
bool useSwitch;
bool periodic;
......@@ -204,7 +210,7 @@ private:
--------------------------------------------------------------------------------------- */
void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
virtual void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) = 0;
/**---------------------------------------------------------------------------------------
......@@ -216,7 +222,7 @@ private:
--------------------------------------------------------------------------------------- */
void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
virtual void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) = 0;
/**
* Compute the displacement and squared distance between two points, optionally using
......@@ -224,26 +230,15 @@ private:
*/
void getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions.
*/
void getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute a fast approximation to erfc(x).
*/
static fvec4 erfcApprox(fvec4 x);
/**
* Create a lookup table for the scale factor used with Ewald and PME.
*/
void tabulateEwaldScaleFactor();
/**
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
* Compute a fast approximation to erfc(x).
*/
fvec4 ewaldScaleFunction(fvec4 x);
static float erfcApprox(float x);
};
} // namespace OpenMM
......
platforms/cpu/include/CpuNonbondedForceVec4.h 0 → 100644
View file @ d4af8747
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef OPENMM_CPU_NONBONDED_FORCE_VEC4_H__
#define OPENMM_CPU_NONBONDED_FORCE_VEC4_H__
#include "CpuNonbondedForce.h"
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class CpuNonbondedForceVec4 : public CpuNonbondedForce {
public:
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
CpuNonbondedForceVec4();
protected:
/**---------------------------------------------------------------------------------------
Calculate all the interactions for one atom block.
@param blockIndex the index of the atom block
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**---------------------------------------------------------------------------------------
Calculate all the interactions for one atom block.
@param blockIndex the index of the atom block
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions.
*/
void getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute a fast approximation to erfc(x).
*/
static fvec4 erfcApprox(fvec4 x);
/**
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
*/
fvec4 ewaldScaleFunction(fvec4 x);
};
} // namespace OpenMM
// ---------------------------------------------------------------------------------------
#endif // OPENMM_CPU_NONBONDED_FORCE_VEC4_H__
platforms/cpu/include/CpuNonbondedForceVec8.h
View file @ d4af8747
......@@ -22,178 +22,23 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef OPENMM_CPU_NONBONDED_FORCE_H__
#define OPENMM_CPU_NONBONDED_FORCE_H__
#ifndef OPENMM_CPU_NONBONDED_FORCE_VEC8_H__
#define OPENMM_CPU_NONBONDED_FORCE_VEC8_H__
#include "AlignedArray.h"
#include "CpuNeighborList.h"
#include "ReferencePairIxn.h"
#include "openmm/internal/ThreadPool.h"
#ifdef __AVX__
#include "CpuNonbondedForce.h"
#include "openmm/internal/vectorize8.h"
#include <set>
#include <utility>
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class CpuNonbondedForceVec8 {
public:
class ComputeDirectTask;
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
class CpuNonbondedForceVec8 : public CpuNonbondedForce {
public:
CpuNonbondedForceVec8();
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
--------------------------------------------------------------------------------------- */
void setUseCutoff(float distance, const CpuNeighborList& neighbors, float solventDielectric);
/**---------------------------------------------------------------------------------------
Set the force to use a switching function on the Lennard-Jones interaction.
@param distance the switching distance
--------------------------------------------------------------------------------------- */
void setUseSwitchingFunction(float distance);
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(float* periodicBoxSize);
/**---------------------------------------------------------------------------------------
Set the force to use Ewald summation.
@param alpha the Ewald separation parameter
@param kmaxx the largest wave vector in the x direction
@param kmaxy the largest wave vector in the y direction
@param kmaxz the largest wave vector in the z direction
--------------------------------------------------------------------------------------- */
void setUseEwald(float alpha, int kmaxx, int kmaxy, int kmaxz);
/**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation.
@param alpha the Ewald separation parameter
@param gridSize the dimensions of the mesh
--------------------------------------------------------------------------------------- */
void setUsePME(float alpha, int meshSize[3]);
/**---------------------------------------------------------------------------------------
Calculate Ewald ixn
@param numberOfAtoms number of atoms
@param posq atom coordinates and charges
@param atomCoordinates atom coordinates (in format needed by PME)
@param atomParameters atom parameters (sigma/2, 2*sqrt(epsilon))
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateReciprocalIxn(int numberOfAtoms, float* posq, const std::vector<RealVec>& atomCoordinates,
const std::vector<std::pair<float, float> >& atomParameters, const std::vector<std::set<int> >& exclusions,
std::vector<RealVec>& forces, double* totalEnergy) const;
/**---------------------------------------------------------------------------------------
Calculate LJ Coulomb pair ixn
@param numberOfAtoms number of atoms
@param posq atom coordinates and charges
@param atomCoordinates atom coordinates (periodic boundary conditions not applied)
@param atomParameters atom parameters (sigma/2, 2*sqrt(epsilon))
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param forces force array (forces added)
@param totalEnergy total energy
@param threads the thread pool to use
--------------------------------------------------------------------------------------- */
void calculateDirectIxn(int numberOfAtoms, float* posq, const std::vector<RealVec>& atomCoordinates, const std::vector<std::pair<float, float> >& atomParameters,
const std::vector<std::set<int> >& exclusions, std::vector<AlignedArray<float> >& threadForce, double* totalEnergy, ThreadPool& threads);
/**
* This routine contains the code executed by each thread.
*/
void threadComputeDirect(ThreadPool& threads, int threadIndex);
private:
bool cutoff;
bool useSwitch;
bool periodic;
bool ewald;
bool pme;
bool tableIsValid;
const CpuNeighborList* neighborList;
float periodicBoxSize[3];
float cutoffDistance, switchingDistance;
float krf, crf;
float alphaEwald;
int numRx, numRy, numRz;
int meshDim[3];
std::vector<float> ewaldScaleTable;
float ewaldDX, ewaldDXInv;
std::vector<double> threadEnergy;
// The following variables are used to make information accessible to the individual threads.
int numberOfAtoms;
float* posq;
RealVec const* atomCoordinates;
std::pair<float, float> const* atomParameters;
std::set<int> const* exclusions;
std::vector<AlignedArray<float> >* threadForce;
bool includeEnergy;
void* atomicCounter;
static const float TWO_OVER_SQRT_PI;
static const int NUM_TABLE_POINTS;
/**---------------------------------------------------------------------------------------
Calculate LJ Coulomb pair ixn between two atoms
@param atom1 the index of the first atom
@param atom2 the index of the second atom
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateOneIxn(int atom1, int atom2, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
protected:
/**---------------------------------------------------------------------------------------
Calculate all the interactions for one atom block.
......@@ -218,12 +63,6 @@ private:
void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Compute the displacement and squared distance between two points, optionally using
* periodic boundary conditions.
*/
void getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions.
......@@ -234,11 +73,6 @@ private:
* Compute a fast approximation to erfc(x).
*/
static fvec8 erfcApprox(fvec8 x);
/**
* Create a lookup table for the scale factor used with Ewald and PME.
*/
void tabulateEwaldScaleFactor();
/**
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
......@@ -250,4 +84,6 @@ private:
// ---------------------------------------------------------------------------------------
#endif // OPENMM_CPU_NONBONDED_FORCE_H__
#endif // __AVX__
#endif // OPENMM_CPU_NONBONDED_FORCE_VEC8_H__
platforms/cpu/sharedTarget/CMakeLists.txt
View file @ d4af8747
SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1")
FOREACH(file ${SOURCE_FILES})
IF (file MATCHES ".*Vec8.*")
SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1 -mavx")
ENDIF (file MATCHES ".*Vec8.*")
ENDFOREACH(file)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
......@@ -7,6 +11,6 @@ ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${PTHREADS_LIB})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1 -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
platforms/cpu/src/CpuKernels.cpp
View file @ d4af8747
......@@ -145,6 +145,22 @@ private:
int numParticles;
};
bool isVec8Supported();
CpuNonbondedForce* createCpuNonbondedForceVec4();
CpuNonbondedForce* createCpuNonbondedForceVec8();
CpuCalcNonbondedForceKernel::CpuCalcNonbondedForceKernel(string name, const Platform& platform, CpuPlatform::PlatformData& data) : CalcNonbondedForceKernel(name, platform),
data(data), bonded14IndexArray(NULL), bonded14ParamArray(NULL), hasInitializedPme(false), neighborList(NULL), nonbonded(NULL) {
if (isVec8Supported) {
neighborList = new CpuNeighborList(8);
nonbonded = createCpuNonbondedForceVec8();
}
else {
neighborList = new CpuNeighborList(4);
nonbonded = createCpuNonbondedForceVec4();
}
}
CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
if (bonded14ParamArray != NULL) {
for (int i = 0; i < num14; i++) {
......@@ -154,6 +170,10 @@ CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
delete bonded14IndexArray;
delete bonded14ParamArray;
}
if (nonbonded != NULL)
delete nonbonded;
if (neighborList != NULL)
delete neighborList;
}
void CpuCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {
......@@ -305,26 +325,26 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
}
}
if (needRecompute) {
neighborList.computeNeighborList(numParticles, posq, exclusions, floatBoxSize, data.isPeriodic, nonbondedCutoff+padding, data.threads);
neighborList->computeNeighborList(numParticles, posq, exclusions, floatBoxSize, data.isPeriodic, nonbondedCutoff+padding, data.threads);
lastPositions = posData;
}
nonbonded.setUseCutoff(nonbondedCutoff, neighborList, rfDielectric);
nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
if (data.isPeriodic) {
double minAllowedSize = 1.999999*nonbondedCutoff;
if (boxSize[0] < minAllowedSize || boxSize[1] < minAllowedSize || boxSize[2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded.setPeriodic(floatBoxSize);
nonbonded->setPeriodic(floatBoxSize);
}
if (ewald)
nonbonded.setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
nonbonded->setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
if (pme)
nonbonded.setUsePME(ewaldAlpha, gridSize);
nonbonded->setUsePME(ewaldAlpha, gridSize);
if (useSwitchingFunction)
nonbonded.setUseSwitchingFunction(switchingDistance);
nonbonded->setUseSwitchingFunction(switchingDistance);
double nonbondedEnergy = 0;
if (includeDirect)
nonbonded.calculateDirectIxn(numParticles, &posq[0], posData, particleParams, exclusions, data.threadForce, includeEnergy ? &nonbondedEnergy : NULL, data.threads);
nonbonded->calculateDirectIxn(numParticles, &posq[0], posData, particleParams, exclusions, data.threadForce, includeEnergy ? &nonbondedEnergy : NULL, data.threads);
if (includeReciprocal) {
if (useOptimizedPme) {
PmeIO io(&posq[0], &data.threadForce[0][0], numParticles);
......@@ -333,7 +353,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
nonbondedEnergy += optimizedPme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
}
else
nonbonded.calculateReciprocalIxn(numParticles, &posq[0], posData, particleParams, exclusions, forceData, includeEnergy ? &nonbondedEnergy : NULL);
nonbonded->calculateReciprocalIxn(numParticles, &posq[0], posData, particleParams, exclusions, forceData, includeEnergy ? &nonbondedEnergy : NULL);
}
energy += nonbondedEnergy;
if (includeDirect) {
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ d4af8747
......@@ -29,7 +29,6 @@
#include "CpuNonbondedForce.h"
#include "ReferenceForce.h"
#include "ReferencePME.h"
#include "openmm/internal/vectorize.h"
#include "gmx_atomic.h"
// In case we're using some primitive version of Visual Studio this will
......@@ -61,6 +60,9 @@ public:
CpuNonbondedForce::CpuNonbondedForce() : cutoff(false), useSwitch(false), periodic(false), ewald(false), pme(false), tableIsValid(false) {
}
CpuNonbondedForce::~CpuNonbondedForce() {
}
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
......@@ -356,7 +358,7 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
float inverseR = 1/r;
float chargeProd = ONE_4PI_EPS0*posq[4*i+3]*posq[4*j+3];
float alphaR = alphaEwald*r;
float erfcAlphaR = erfcApprox(alphaR)[0];
float erfcAlphaR = erfcApprox(alphaR);
float dEdR = (float) (chargeProd * inverseR * inverseR * inverseR);
dEdR = (float) (dEdR * (1.0f-erfcAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
fvec4 result = deltaR*dEdR;
......@@ -446,222 +448,6 @@ void CpuNonbondedForce::calculateOneIxn(int ii, int jj, float* forces, double* t
(fvec4(forces+4*jj)-result).store(forces+4*jj);
}
void CpuNonbondedForce::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block.
int blockAtom[4];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor.
int atom = neighbors[i];
// Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2;
getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include;
char excl = exclusions[i];
if (excl == 0)
include = -1;
else
include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
include = include & (r2 < cutoffDistance*cutoffDistance);
if (!any(include))
continue; // No interactions to compute.
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
fvec4 sig = blockAtomSigma+atomParameters[atom].first;
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f);
if (useSwitch) {
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
dEdR = switchValue*dEdR - energy*switchDeriv*r;
energy *= switchValue;
}
}
else {
energy = 0.0f;
dEdR = 0.0f;
}
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
if (cutoff)
dEdR += chargeProd*(inverseR-2.0f*krf*r2);
else
dEdR += chargeProd*inverseR;
dEdR *= inverseR*inverseR;
// Accumulate energies.
fvec4 one(1.0f);
if (totalEnergy) {
if (cutoff)
energy += chargeProd*(inverseR+krf*r2-crf);
else
energy += chargeProd*inverseR;
energy = blend(0.0f, energy, include);
*totalEnergy += dot4(energy, one);
}
// Accumulate forces.
dEdR = blend(0.0f, dEdR, include);
fvec4 fx = dx*dEdR;
fvec4 fy = dy*dEdR;
fvec4 fz = dz*dEdR;
blockAtomForceX += fx;
blockAtomForceY += fy;
blockAtomForceZ += fz;
float* atomForce = forces+4*atom;
atomForce[0] -= dot4(fx, one);
atomForce[1] -= dot4(fy, one);
atomForce[2] -= dot4(fz, one);
}
// Record the forces on the block atoms.
fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
transpose(f[0], f[1], f[2], f[3]);
for (int j = 0; j < 4; j++)
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}
void CpuNonbondedForce::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block.
int blockAtom[4];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor.
int atom = neighbors[i];
// Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2;
getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include;
char excl = exclusions[i];
if (excl == 0)
include = -1;
else
include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
include = include & (r2 < cutoffDistance*cutoffDistance);
if (!any(include))
continue; // No interactions to compute.
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
fvec4 sig = blockAtomSigma+atomParameters[atom].first;
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f);
if (useSwitch) {
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
dEdR = switchValue*dEdR - energy*switchDeriv*r;
energy *= switchValue;
}
}
else {
energy = 0.0f;
dEdR = 0.0f;
}
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
dEdR += chargeProd*inverseR*ewaldScaleFunction(r);
dEdR *= inverseR*inverseR;
// Accumulate energies.
fvec4 one(1.0f);
if (totalEnergy) {
energy += chargeProd*inverseR*erfcApprox(alphaEwald*r);
energy = blend(0.0f, energy, include);
*totalEnergy += dot4(energy, one);
}
// Accumulate forces.
dEdR = blend(0.0f, dEdR, include);
fvec4 fx = dx*dEdR;
fvec4 fy = dy*dEdR;
fvec4 fz = dz*dEdR;
blockAtomForceX += fx;
blockAtomForceY += fy;
blockAtomForceZ += fz;
float* atomForce = forces+4*atom;
atomForce[0] -= dot4(fx, one);
atomForce[1] -= dot4(fy, one);
atomForce[2] -= dot4(fz, one);
}
// Record the forces on the block atoms.
fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
transpose(f[0], f[1], f[2], f[3]);
for (int j = 0; j < 4; j++)
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}
void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
deltaR = posJ-posI;
if (periodic) {
......@@ -671,41 +457,15 @@ void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& d
r2 = dot3(deltaR, deltaR);
}
void CpuNonbondedForce::getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0];
dy = y-posI[1];
dz = z-posI[2];
if (periodic) {
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
r2 = dx*dx + dy*dy + dz*dz;
}
fvec4 CpuNonbondedForce::erfcApprox(fvec4 x) {
float CpuNonbondedForce::erfcApprox(float x) {
// This approximation for erfc is from Abramowitz and Stegun (1964) p. 299. They cite the following as
// the original source: C. Hastings, Jr., Approximations for Digital Computers (1955). It has a maximum
// error of 3e-7.
fvec4 t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x;
float t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x;
t *= t;
t *= t;
t *= t;
return 1.0f/(t*t);
}
fvec4 CpuNonbondedForce::ewaldScaleFunction(fvec4 x) {
// Compute the tabulated Ewald scale factor: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
fvec4 x1 = x*ewaldDXInv;
ivec4 index = min(floor(x1), NUM_TABLE_POINTS);
fvec4 coeff2 = x1-index;
fvec4 coeff1 = 1.0f-coeff2;
fvec4 t1(&ewaldScaleTable[index[0]]);
fvec4 t2(&ewaldScaleTable[index[1]]);
fvec4 t3(&ewaldScaleTable[index[2]]);
fvec4 t4(&ewaldScaleTable[index[3]]);
transpose(t1, t2, t3, t4);
return coeff1*t1 + coeff2*t2;
}
platforms/cpu/src/CpuNonbondedForceVec4.cpp 0 → 100644
View file @ d4af8747
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec4.h"
using namespace std;
using namespace OpenMM;
/**
* Factory method to create a CpuNonbondedForceVec4.
*/
CpuNonbondedForce* createCpuNonbondedForceVec4() {
return new CpuNonbondedForceVec4();
}
/**---------------------------------------------------------------------------------------
CpuNonbondedForceVec4 constructor
--------------------------------------------------------------------------------------- */
CpuNonbondedForceVec4::CpuNonbondedForceVec4() {
}
void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block.
int blockAtom[4];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor.
int atom = neighbors[i];
// Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2;
getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include;
char excl = exclusions[i];
if (excl == 0)
include = -1;
else
include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
include = include & (r2 < cutoffDistance*cutoffDistance);
if (!any(include))
continue; // No interactions to compute.
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
fvec4 sig = blockAtomSigma+atomParameters[atom].first;
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f);
if (useSwitch) {
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
dEdR = switchValue*dEdR - energy*switchDeriv*r;
energy *= switchValue;
}
}
else {
energy = 0.0f;
dEdR = 0.0f;
}
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
if (cutoff)
dEdR += chargeProd*(inverseR-2.0f*krf*r2);
else
dEdR += chargeProd*inverseR;
dEdR *= inverseR*inverseR;
// Accumulate energies.
fvec4 one(1.0f);
if (totalEnergy) {
if (cutoff)
energy += chargeProd*(inverseR+krf*r2-crf);
else
energy += chargeProd*inverseR;
energy = blend(0.0f, energy, include);
*totalEnergy += dot4(energy, one);
}
// Accumulate forces.
dEdR = blend(0.0f, dEdR, include);
fvec4 fx = dx*dEdR;
fvec4 fy = dy*dEdR;
fvec4 fz = dz*dEdR;
blockAtomForceX += fx;
blockAtomForceY += fy;
blockAtomForceZ += fz;
float* atomForce = forces+4*atom;
atomForce[0] -= dot4(fx, one);
atomForce[1] -= dot4(fy, one);
atomForce[2] -= dot4(fz, one);
}
// Record the forces on the block atoms.
fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
transpose(f[0], f[1], f[2], f[3]);
for (int j = 0; j < 4; j++)
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}
void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block.
int blockAtom[4];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
// Loop over neighbors for this block.
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor.
int atom = neighbors[i];
// Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2;
getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include;
char excl = exclusions[i];
if (excl == 0)
include = -1;
else
include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
include = include & (r2 < cutoffDistance*cutoffDistance);
if (!any(include))
continue; // No interactions to compute.
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 energy, dEdR;
float atomEpsilon = atomParameters[atom].second;
if (atomEpsilon != 0.0f) {
fvec4 sig = blockAtomSigma+atomParameters[atom].first;
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
dEdR = epsSig6*(12.0f*sig6 - 6.0f);
energy = epsSig6*(sig6-1.0f);
if (useSwitch) {
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
dEdR = switchValue*dEdR - energy*switchDeriv*r;
energy *= switchValue;
}
}
else {
energy = 0.0f;
dEdR = 0.0f;
}
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
dEdR += chargeProd*inverseR*ewaldScaleFunction(r);
dEdR *= inverseR*inverseR;
// Accumulate energies.
fvec4 one(1.0f);
if (totalEnergy) {
energy += chargeProd*inverseR*erfcApprox(alphaEwald*r);
energy = blend(0.0f, energy, include);
*totalEnergy += dot4(energy, one);
}
// Accumulate forces.
dEdR = blend(0.0f, dEdR, include);
fvec4 fx = dx*dEdR;
fvec4 fy = dy*dEdR;
fvec4 fz = dz*dEdR;
blockAtomForceX += fx;
blockAtomForceY += fy;
blockAtomForceZ += fz;
float* atomForce = forces+4*atom;
atomForce[0] -= dot4(fx, one);
atomForce[1] -= dot4(fy, one);
atomForce[2] -= dot4(fz, one);
}
// Record the forces on the block atoms.
fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
transpose(f[0], f[1], f[2], f[3]);
for (int j = 0; j < 4; j++)
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}
void CpuNonbondedForceVec4::getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0];
dy = y-posI[1];
dz = z-posI[2];
if (periodic) {
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
r2 = dx*dx + dy*dy + dz*dz;
}
fvec4 CpuNonbondedForceVec4::erfcApprox(fvec4 x) {
// This approximation for erfc is from Abramowitz and Stegun (1964) p. 299. They cite the following as
// the original source: C. Hastings, Jr., Approximations for Digital Computers (1955). It has a maximum
// error of 3e-7.
fvec4 t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x;
t *= t;
t *= t;
t *= t;
return 1.0f/(t*t);
}
fvec4 CpuNonbondedForceVec4::ewaldScaleFunction(fvec4 x) {
// Compute the tabulated Ewald scale factor: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
fvec4 x1 = x*ewaldDXInv;
ivec4 index = min(floor(x1), NUM_TABLE_POINTS);
fvec4 coeff2 = x1-index;
fvec4 coeff1 = 1.0f-coeff2;
fvec4 t1(&ewaldScaleTable[index[0]]);
fvec4 t2(&ewaldScaleTable[index[1]]);
fvec4 t3(&ewaldScaleTable[index[2]]);
fvec4 t4(&ewaldScaleTable[index[3]]);
transpose(t1, t2, t3, t4);
return coeff1*t1 + coeff2*t2;
}
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ d4af8747
......@@ -22,429 +22,53 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <complex>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec8.h"
#include "ReferenceForce.h"
#include "ReferencePME.h"
#include "openmm/internal/vectorize.h"
#include "gmx_atomic.h"
// In case we're using some primitive version of Visual Studio this will
// make sure that erf() and erfc() are defined.
#include "openmm/internal/MSVC_erfc.h"
#include "openmm/internal/hardware.h"
using namespace std;
using namespace OpenMM;
const float CpuNonbondedForceVec8::TWO_OVER_SQRT_PI = (float) (2/sqrt(PI_M));
const int CpuNonbondedForceVec8::NUM_TABLE_POINTS = 2048;
class CpuNonbondedForceVec8::ComputeDirectTask : public ThreadPool::Task {
public:
ComputeDirectTask(CpuNonbondedForceVec8& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeDirect(threads, threadIndex);
}
CpuNonbondedForceVec8& owner;
};
/**---------------------------------------------------------------------------------------
CpuNonbondedForceVec8 constructor
--------------------------------------------------------------------------------------- */
CpuNonbondedForceVec8::CpuNonbondedForceVec8() : cutoff(false), useSwitch(false), periodic(false), ewald(false), pme(false), tableIsValid(false) {
#ifndef __AVX__
bool isVec8Supported() {
return false;
}
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
--------------------------------------------------------------------------------------- */
void CpuNonbondedForceVec8::setUseCutoff(float distance, const CpuNeighborList& neighbors, float solventDielectric) {
if (distance != cutoffDistance)
tableIsValid = false;
cutoff = true;
cutoffDistance = distance;
neighborList = &neighbors;
krf = pow(cutoffDistance, -3.0f)*(solventDielectric-1.0)/(2.0*solventDielectric+1.0);
crf = (1.0/cutoffDistance)*(3.0*solventDielectric)/(2.0*solventDielectric+1.0);
}
/**---------------------------------------------------------------------------------------
Set the force to use a switching function on the Lennard-Jones interaction.
@param distance the switching distance
--------------------------------------------------------------------------------------- */
void CpuNonbondedForceVec8::setUseSwitchingFunction(float distance) {
useSwitch = true;
switchingDistance = distance;
CpuNonbondedForce* createCpuNonbondedForceVec8() {
throw OpenMMException("Internal error: OpenMM was compiled without AVX support");
}
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
also been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
--------------------------------------------------------------------------------------- */
void CpuNonbondedForceVec8::setPeriodic(float* periodicBoxSize) {
assert(cutoff);
assert(periodicBoxSize[0] >= 2*cutoffDistance);
assert(periodicBoxSize[1] >= 2*cutoffDistance);
assert(periodicBoxSize[2] >= 2*cutoffDistance);
periodic = true;
this->periodicBoxSize[0] = periodicBoxSize[0];
this->periodicBoxSize[1] = periodicBoxSize[1];
this->periodicBoxSize[2] = periodicBoxSize[2];
}
/**---------------------------------------------------------------------------------------
Set the force to use Ewald summation.
@param alpha the Ewald separation parameter
@param kmaxx the largest wave vector in the x direction
@param kmaxy the largest wave vector in the y direction
@param kmaxz the largest wave vector in the z direction
--------------------------------------------------------------------------------------- */
void CpuNonbondedForceVec8::setUseEwald(float alpha, int kmaxx, int kmaxy, int kmaxz) {
if (alpha != alphaEwald)
tableIsValid = false;
alphaEwald = alpha;
numRx = kmaxx;
numRy = kmaxy;
numRz = kmaxz;
ewald = true;
tabulateEwaldScaleFactor();
}
/**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation.
@param alpha the Ewald separation parameter
@param gridSize the dimensions of the mesh
--------------------------------------------------------------------------------------- */
void CpuNonbondedForceVec8::setUsePME(float alpha, int meshSize[3]) {
if (alpha != alphaEwald)
tableIsValid = false;
alphaEwald = alpha;
meshDim[0] = meshSize[0];
meshDim[1] = meshSize[1];
meshDim[2] = meshSize[2];
pme = true;
tabulateEwaldScaleFactor();
}
void CpuNonbondedForceVec8::tabulateEwaldScaleFactor() {
if (tableIsValid)
return;
tableIsValid = true;
ewaldDX = cutoffDistance/NUM_TABLE_POINTS;
ewaldDXInv = 1.0f/ewaldDX;
ewaldScaleTable.resize(NUM_TABLE_POINTS+4);
for (int i = 0; i < NUM_TABLE_POINTS+4; i++) {
double r = i*ewaldDX;
double alphaR = alphaEwald*r;
ewaldScaleTable[i] = erfc(alphaR) + TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR);
}
}
void CpuNonbondedForceVec8::calculateReciprocalIxn(int numberOfAtoms, float* posq, const vector<RealVec>& atomCoordinates,
const vector<pair<float, float> >& atomParameters, const vector<set<int> >& exclusions,
vector<RealVec>& forces, double* totalEnergy) const {
typedef std::complex<float> d_complex;
static const float epsilon = 1.0;
int kmax = (ewald ? std::max(numRx, std::max(numRy,numRz)) : 0);
float factorEwald = -1 / (4*alphaEwald*alphaEwald);
float TWO_PI = 2.0 * PI_M;
float recipCoeff = (float)(ONE_4PI_EPS0*4*PI_M/(periodicBoxSize[0] * periodicBoxSize[1] * periodicBoxSize[2]) /epsilon);
if (pme) {
pme_t pmedata;
RealOpenMM virial[3][3];
pme_init(&pmedata, alphaEwald, numberOfAtoms, meshDim, 5, 1);
vector<RealOpenMM> charges(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++)
charges[i] = posq[4*i+3];
RealOpenMM boxSize[3] = {periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2]};
RealOpenMM recipEnergy = 0.0;
pme_exec(pmedata, atomCoordinates, forces, charges, boxSize, &recipEnergy, virial);
if (totalEnergy)
*totalEnergy += recipEnergy;
pme_destroy(pmedata);
}
// Ewald method
else if (ewald) {
// setup reciprocal box
float recipBoxSize[3] = { TWO_PI / periodicBoxSize[0], TWO_PI / periodicBoxSize[1], TWO_PI / periodicBoxSize[2]};
// setup K-vectors
#define EIR(x, y, z) eir[(x)*numberOfAtoms*3+(y)*3+z]
vector<d_complex> eir(kmax*numberOfAtoms*3);
vector<d_complex> tab_xy(numberOfAtoms);
vector<d_complex> tab_qxyz(numberOfAtoms);
for (int i = 0; (i < numberOfAtoms); i++) {
float* pos = posq+4*i;
for (int m = 0; (m < 3); m++)
EIR(0, i, m) = d_complex(1,0);
for (int m=0; (m<3); m++)
EIR(1, i, m) = d_complex(cos(pos[m]*recipBoxSize[m]),
sin(pos[m]*recipBoxSize[m]));
for (int j=2; (j<kmax); j++)
for (int m=0; (m<3); m++)
EIR(j, i, m) = EIR(j-1, i, m) * EIR(1, i, m);
}
// calculate reciprocal space energy and forces
int lowry = 0;
int lowrz = 1;
for (int rx = 0; rx < numRx; rx++) {
float kx = rx * recipBoxSize[0];
for (int ry = lowry; ry < numRy; ry++) {
float ky = ry * recipBoxSize[1];
if (ry >= 0) {
for (int n = 0; n < numberOfAtoms; n++)
tab_xy[n] = EIR(rx, n, 0) * EIR(ry, n, 1);
}
else {
for (int n = 0; n < numberOfAtoms; n++)
tab_xy[n]= EIR(rx, n, 0) * conj (EIR(-ry, n, 1));
}
for (int rz = lowrz; rz < numRz; rz++) {
if (rz >= 0) {
for (int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = posq[4*n+3] * (tab_xy[n] * EIR(rz, n, 2));
}
else {
for (int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = posq[4*n+3] * (tab_xy[n] * conj(EIR(-rz, n, 2)));
}
float cs = 0.0f;
float ss = 0.0f;
for (int n = 0; n < numberOfAtoms; n++) {
cs += tab_qxyz[n].real();
ss += tab_qxyz[n].imag();
}
float kz = rz * recipBoxSize[2];
float k2 = kx * kx + ky * ky + kz * kz;
float ak = exp(k2*factorEwald) / k2;
for (int n = 0; n < numberOfAtoms; n++) {
float force = ak * (cs * tab_qxyz[n].imag() - ss * tab_qxyz[n].real());
forces[n][0] += 2 * recipCoeff * force * kx;
forces[n][1] += 2 * recipCoeff * force * ky;
forces[n][2] += 2 * recipCoeff * force * kz;
}
if (totalEnergy)
*totalEnergy += recipCoeff * ak * (cs * cs + ss * ss);
lowrz = 1 - numRz;
}
lowry = 1 - numRy;
}
}
}
}
void CpuNonbondedForceVec8::calculateDirectIxn(int numberOfAtoms, float* posq, const vector<RealVec>& atomCoordinates, const vector<pair<float, float> >& atomParameters,
const vector<set<int> >& exclusions, vector<AlignedArray<float> >& threadForce, double* totalEnergy, ThreadPool& threads) {
// Record the parameters for the threads.
this->numberOfAtoms = numberOfAtoms;
this->posq = posq;
this->atomCoordinates = &atomCoordinates[0];
this->atomParameters = &atomParameters[0];
this->exclusions = &exclusions[0];
this->threadForce = &threadForce;
includeEnergy = (totalEnergy != NULL);
threadEnergy.resize(threads.getNumThreads());
gmx_atomic_t counter;
gmx_atomic_set(&counter, 0);
this->atomicCounter = &counter;
// Signal the threads to start running and wait for them to finish.
ComputeDirectTask task(*this);
threads.execute(task);
threads.waitForThreads();
// Combine the energies from all the threads.
#else
/**
* Check whether 8 component vectors are supported with the current CPU.
*/
bool isVec8Supported() {
// Make sure the CPU supports AVX.
if (totalEnergy != NULL) {
double directEnergy = 0;
int numThreads = threads.getNumThreads();
for (int i = 0; i < numThreads; i++)
directEnergy += threadEnergy[i];
*totalEnergy += directEnergy;
int cpuInfo[4];
cpuid(cpuInfo, 0);
if (cpuInfo[0] >= 1) {
cpuid(cpuInfo, 1);
return ((cpuInfo[2] & ((int) 1 << 28)) != 0);
}
return false;
}
void CpuNonbondedForceVec8::threadComputeDirect(ThreadPool& threads, int threadIndex) {
// Compute this thread's subset of interactions.
int numThreads = threads.getNumThreads();
threadEnergy[threadIndex] = 0;
double* energyPtr = (includeEnergy ? &threadEnergy[threadIndex] : NULL);
float* forces = &(*threadForce)[threadIndex][0];
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
if (ewald || pme) {
// Compute the interactions from the neighbor list.
while (true) {
int nextBlock = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (nextBlock >= neighborList->getNumBlocks())
break;
calculateBlockEwaldIxn(nextBlock, forces, energyPtr, boxSize, invBoxSize);
}
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
for (int i = threadIndex; i < numberOfAtoms; i += numThreads) {
fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f);
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
if (*iter > i) {
int j = *iter;
fvec4 deltaR;
fvec4 posJ((float) atomCoordinates[j][0], (float) atomCoordinates[j][1], (float) atomCoordinates[j][2], 0.0f);
float r2;
getDeltaR(posJ, posI, deltaR, r2, false, boxSize, invBoxSize);
float r = sqrtf(r2);
float inverseR = 1/r;
float chargeProd = ONE_4PI_EPS0*posq[4*i+3]*posq[4*j+3];
float alphaR = alphaEwald*r;
float erfcAlphaR = erfcApprox(alphaR).lowerVec()[0];
float dEdR = (float) (chargeProd * inverseR * inverseR * inverseR);
dEdR = (float) (dEdR * (1.0f-erfcAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
fvec4 result = deltaR*dEdR;
(fvec4(forces+4*i)-result).store(forces+4*i);
(fvec4(forces+4*j)+result).store(forces+4*j);
if (includeEnergy)
threadEnergy[threadIndex] -= chargeProd*inverseR*(1.0f-erfcAlphaR);
}
}
}
}
else if (cutoff) {
// Compute the interactions from the neighbor list.
while (true) {
int nextBlock = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (nextBlock >= neighborList->getNumBlocks())
break;
calculateBlockIxn(nextBlock, forces, energyPtr, boxSize, invBoxSize);
}
}
else {
// Loop over all atom pairs
while (true) {
int i = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (i >= numberOfAtoms)
break;
for (int j = i+1; j < numberOfAtoms; j++)
if (exclusions[j].find(i) == exclusions[j].end())
calculateOneIxn(i, j, forces, energyPtr, boxSize, invBoxSize);
}
}
/**
* Factory method to create a CpuNonbondedForceVec8.
*/
CpuNonbondedForce* createCpuNonbondedForceVec8() {
return new CpuNonbondedForceVec8();
}
void CpuNonbondedForceVec8::calculateOneIxn(int ii, int jj, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// get deltaR, R2, and R between 2 atoms
fvec4 deltaR;
fvec4 posI(posq+4*ii);
fvec4 posJ(posq+4*jj);
float r2;
getDeltaR(posJ, posI, deltaR, r2, periodic, boxSize, invBoxSize);
if (cutoff && r2 >= cutoffDistance*cutoffDistance)
return;
float r = sqrtf(r2);
float inverseR = 1/r;
float switchValue = 1, switchDeriv = 0;
if (useSwitch && r > switchingDistance) {
float t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
switchValue = 1+t*t*t*(-10+t*(15-t*6));
switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
}
float sig = atomParameters[ii].first + atomParameters[jj].first;
float sig2 = inverseR*sig;
sig2 *= sig2;
float sig6 = sig2*sig2*sig2;
float eps = atomParameters[ii].second*atomParameters[jj].second;
float dEdR = switchValue*eps*(12.0f*sig6 - 6.0f)*sig6;
float chargeProd = ONE_4PI_EPS0*posq[4*ii+3]*posq[4*jj+3];
if (cutoff)
dEdR += (float) (chargeProd*(inverseR-2.0f*krf*r2));
else
dEdR += (float) (chargeProd*inverseR);
dEdR *= inverseR*inverseR;
float energy = eps*(sig6-1.0f)*sig6;
if (useSwitch) {
dEdR -= energy*switchDeriv*inverseR;
energy *= switchValue;
}
// accumulate energies
/**---------------------------------------------------------------------------------------
if (totalEnergy) {
if (cutoff)
energy += (float) (chargeProd*(inverseR+krf*r2-crf));
else
energy += (float) (chargeProd*inverseR);
*totalEnergy += energy;
}
CpuNonbondedForceVec8 constructor
// accumulate forces
--------------------------------------------------------------------------------------- */
fvec4 result = deltaR*dEdR;
(fvec4(forces+4*ii)+result).store(forces+4*ii);
(fvec4(forces+4*jj)-result).store(forces+4*jj);
}
CpuNonbondedForceVec8::CpuNonbondedForceVec8() {
}
void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block.
......@@ -660,15 +284,6 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}
void CpuNonbondedForceVec8::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
deltaR = posJ-posI;
if (periodic) {
fvec4 base = round(deltaR*invBoxSize)*boxSize;
deltaR = deltaR-base;
}
r2 = dot3(deltaR, deltaR);
}
void CpuNonbondedForceVec8::getDeltaR(const float* posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0];
dy = y-posI[1];
......@@ -714,3 +329,4 @@ fvec8 CpuNonbondedForceVec8::ewaldScaleFunction(fvec8 x) {
transpose(t1, t2, t3, t4, t5, t6, t7, t8, s1, s2, s3, s4);
return coeff1*s1 + coeff2*s2;
}
#endif
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment